The present invention relates to a mass spectrometer and a method of mass spectrometry.
Tandem mass spectrometry or MS/MS has become the preferred technology for many applications in which mass spectrometry plays a part. Firstly, tandem mass spectrometry allows selection and isolation of specific compounds of interest and their subsequent identification. Secondly, the extra selectivity of MS/MS enables this technology to be used for quantification of target compounds even in the presence of complex matrices.
A known tandem mass spectrometer comprises two mass filters or analysers arranged in series with a collision cell arranged in between the two mass filters or analysers. Ions selected by the first mass filter are arranged to undergo collision-induced decomposition (CID) in the collision cell wherein ions undergo collisions with gas molecules. The second mass analyser is arranged to analyse the products of the fragmentation process. The processes of mass selection, fragmentation and product ion mass analysis take place sequentially in space.
The most common form of tandem mass spectrometer is generally known as a triple quadrupole mass spectrometer. A triple quadrupole tandem mass spectrometer comprises a first quadrupole mass filter (MS1) followed by a gas collision cell. The gas collision cell is followed by a second quadrupole mass filter (MS2). The name triple quadrupole is derived from the first such instrument in which a RF quadrupole rod set ion guide was used as the gas collision cell. The quadrupole mass filters are typically used to transmit ions having a specific mass to charge ratio. Therefore, in order to record a full mass spectrum, the quadrupole mass filters must be scanned across the full mass to charge ratio spectrum in order to transmit ions sequentially having different mass to charge ratios. The duty cycle for this process is therefore relatively low and as a consequence the sensitivity of the quadrupole mass filter used to record a full spectrum is relatively poor. On the other hand, the quadrupole mass filter will have 100% duty cycle when used to transmit ions having a specific mass to charge ratio.
A triple quadrupole mass spectrometer may be used in a Selected Reaction Monitoring (“SRM”) mode of operation wherein ions having a single mass to charge ratio are transmitted through the first mass filter (MS1) and the second mass filter (MS2) is set to monitor for fragment or daughter ions having a specific mass to charge ratio. Such an arrangement is very specific and exceptionally sensitive. Triple quadrupole mass spectrometers have, as a result, found significant use in drug discovery and development processes where they may be used either in a Selected Reaction Monitoring mode of operation or in either a related Multiple Reaction Monitoring (“MRM”) mode of operation to quantify target compounds of biological significance.
More recently, triple quadrupole mass spectrometers have been used in the study of protein biomarkers. For example, a protein extract may be analysed to determine which proteins may be used as biomarkers in order to indicate the occurrence of a specific medical disorder or to measure the response to specific medication. Such biomarkers may subsequently be monitored as an aid to medical diagnosis and/or as a means of monitoring therapeutic response. A sample may first be extracted from biological fluids or tissue e.g. blood plasma or serum, urine, saliva, body tissue etc. Proteins, or a sub-group of proteins, may then be extracted from the biological fluid or tissue using one or more known extraction methods e.g. methods based on protein size, polarity, solubility, hydrophobicity, chemical affinity, molecular affinity etc. The resulting protein mixture may then be digested (for example using the digestion enzyme trypsin) and the resulting mixture of peptides is then submitted for separation by chromatography and analysis by mass spectrometry.
The peptide mixture may typically be separated by liquid chromatography. The individual components eluting from the chromatography column may be ionised by, for example, Electrospray ionisation. Specific targeted peptides may be detected by mass spectrometry e.g. by using a triple quadrupole mass spectrometer operating in a Selected Reaction Monitoring (SRM) mode of operation. As already discussed, such an arrangement provides a very specific and a very sensitive method of analysis which is also capable of accurately quantifying the amount of the targeted peptides present. This in turn may be used to quantify the amount of specific targeted proteins present in the original sample.
Despite the high specificity and the high sensitivity of the known method, detection limits and quantification limits are still often imposed by chemical background present in the protein digest. The peptides eluting from the chromatography column and subsequently ionised by Electrospray ionisation will commonly give rise to doubly or triply charged ions but other material eluting from the chromatography column at the same time will commonly yield a low background level of singly charged ions throughout the mass spectrum. As a consequence, singly charged chemical matrix background ions having similar mass to charge ratios as the targeted peptides will also appear in the resulting mass spectrum. This can, in some situations, impose a limitation on the detection and quantification of some of the targeted peptides. In some instances, where the protein relative abundance is very low, the peptide ions of interest may be totally obscured by background chemical matrix ions.
It is therefore desired to provide an improved mass spectrometer and method of mass spectrometry.